


Conscience Doth Make Cowards of Us All

by jdale



Series: Rent Asunder [1]
Category: Stargate Atlantis
Genre: Angst, Elements of a Post-Trinity Fic, Episode: s04e01 Adrift, Episode: s04e02 Lifeline, Except Set a Lot Further Down the Road, F/M, Fix-It of Sorts, Infighting, Sad Ending, Things left unsaid, Unhappy Ending
Language: English
Status: Completed
Published: 2019-10-21
Updated: 2019-10-21
Packaged: 2020-12-31 07:56:53
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 1
Words: 2,019
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/21122426
Author URL: https://archiveofourown.org/users/jdale/pseuds/jdale
Summary: The things John and Elizabeth wanted to say but didn’t, because they knew they would only make it harder to say goodbye.





	Conscience Doth Make Cowards of Us All

**Author's Note:**

> I’ve always hated the way canon leaves Elizabeth in limbo not once but twice, and especially the first time, because the fact that John didn’t even _try_ to mount a rescue goes completely against everything we know about his character up to this point. So I guess this is sort of a twisted fix-it in the sense that it gives her story a proper ending rather than just leaving her hanging?
> 
> Also, I think McKay’s decision to reactivate the nanites, and his handling of that whole situation in general, is very reminiscent of some of the behavior we see from him in “Trinity,” so I’ve decided to address that here as well.
> 
> Some lines taken directly from SGA 4x01 “Adrift” and 4x02 “Lifeline.” Also note that I have skipped over some events that are essentially unchanged from how they occurred in canon, so parts of the story may not make sense if you haven’t seen those two episodes.

“_What did you do?_” John growled.

McKay glanced over at Keller as if saying, ‘you tell him.’ When it became clear she wasn’t going to, he replied, “I reactivated the nanites.”

It was all John could do to stop himself from punching the scientist’s lights out. “_Dammit_, McKay!”

“Look, you were busy!” McKay protested. “It was life or death! If I didn’t act—”

“She would’ve died, yes,” John interrupted mockingly. “Don’t you think I knew that when I told you _not to do it_?”

“Okay, I know what you’re thinking, but helping Elizabeth is not putting us at risk!” McKay assured him.

_You know, for a so-called genius, you can be a real numbnuts at times,_ John thought, glad that he didn’t have his sidearm on him for fear of what he might have done if he did. “You just reactivated the Replicator nanites!”

“They’re harmless!” McKay replied. “Look, I am a hundred percent certain they’re not going to try to take her over or contact the others!”

“Just like you were a hundred percent certain you could stabilize a containment field not even the Ancients could make work?” John shot back.

McKay’s features twisted into an enraged snarl as he took a wild swing at John’s head. John dodged the punch easily and caught McKay’s arm to prevent him from making any further attempts.

“Shut it down,” John ordered.

McKay’s mouth dropped open in shock. “But—that would _kill_ her!”

_No shit, Sherlock,_ John thought. “McKay, get out of your own damn head for a moment and actually _think_ about this! Do you really think Elizabeth would want to spend the rest of her life with her body partially under the control of Replicator nanites that could force her to turn on us at any time?”

“As I’ve already told you, Sheppard, they’re not going to try to take control of her!” McKay reminded him.

“I don’t care what you say; you can’t _possibly_ know that for sure!” John replied. “And regardless of that, she would not have wanted you to reactivate those nanites under _any circumstances_, not even if the alternative was certain death!”

“She would’ve done it for you if the roles were reversed!” McKay argued.

John shook his head, refusing to engage in that debate. “Shut it down. _Now_.”

McKay crossed his arms defiantly. “No. No, I’m not going to.”

John’s fists clenched at his sides. “Doctor McKay, as acting leader of this expedition, I am giving you a _direct order_ to shut down those nanites.”

“I’m not military,” McKay shot back. “You can’t _order_ me to do anything.”

John touched his earpiece. “Meyers, bring an EMP generator to the OR.”

Before McKay could formulate a response, a nurse called from inside Elizabeth’s room, “Doctor Keller?”

The two of them put their argument aside and went into the room, Ronon and Keller trailing behind. Elizabeth was sitting up on the bed, looking in confusion at the bandages that had been around her head, which she now held in her hand.

“John? Rodney?” she asked fearfully. “What’s going on?”

John’s frustration with the current situation was evident in the tone of his response. “What’s going on is that _shit-for-brains_ over here,” he jabbed his thumb at McKay, “reactivated your nanites even after I _explicitly told him not to_!”

“That’s not true,” Rodney accused. “You said not to do it unless I was sure I could reprogram the nanites to act only as replacements for her damaged cells and do nothing else.”

“And what the hell possessed you to think it would ever be _possible_ for you to _be_ sure?” Elizabeth exploded. “Did the last time you tried to do something even the _Ancients_ couldn’t do teach you _nothing_?”

“Will you _stop_ bringing that up?” Rodney screamed, looking ready to throttle someone. “It was _one damn time_!”

“That you clearly didn’t learn your lesson from, or else you wouldn’t have put the entire city at risk by reactivating the nanites!” John pointed out.

“Do you have any idea the _hell_ I went through the last time I had these things running around in my system?” Elizabeth asked. “I don’t care if you think they are safe; I would rather die as a human than live as some…_cyborg_, especially if there’s even the remotest possibility the collective could find a way to hijack my body and force me to turn on you.”

“Dammit, Elizabeth!” McKay’s anger was turning to tears. “I couldn’t do anything when Carson died; I am not about to stand idly by and watch another of the few friends I have in this universe die on me, not when there’s something I can do about it this time.”

John seized on his opportunity. “Well, _all_ of your friends are going to die if we can’t somehow find enough power to get the city back into hyperspace, so maybe that should be the bigger priority right now?”

McKay nodded, wiping his eyes on his sleeve. “Right, right. Save the city first, then save Elizabeth. I’ll be in the control room if you need me.”

* * *

“I’ve managed to install a rudimentary hyperdrive in one of the Puddle Jumpers,” McKay explained. “It can’t jump very far, and it won’t last very many jumps, but it should be enough to get us to the Replicator homeworld and then get us back to Atlantis once we’ve stolen a ZPM to power the city’s shields and hyperdrive.”

“And you want to put me at even greater risk of being taken over by the Replicators by bringing me along on this mission?” Elizabeth asked skeptically.

“Look, I wouldn’t be proposing this if I didn’t think it was our only viable option,” McKay shot back. “Once we get there, we’ll be able to use your nanites to hack into the Replicator mainframe, locate the closest ZPM to our landing site, and track the Replicators’ movements so we can avoid being discovered on our way there.”

“And what happens if the nanites are able to take control of me?” Elizabeth pressed.

“Well, that won’t happen,” McKay assured her. “I would block any attempt—”

“And if they manage to defeat your attempts at blocking them?”

“I ordered McKay to write a kill switch into the nanites’ code,” John told her. “If we activate it, it’ll shut the nanites down.”

“A good thought, but if the Replicators have any sense at all, disabling the kill switch will be the first thing they do after they take control of me,” Elizabeth pointed out. “There needs to be a backup plan.”

“P90 shot to the head,” John proposed. “Enough of you is still flesh and bone that bullets should still work.”

Elizabeth nodded. “Alright, but at the first sign of anything even remotely out of the ordinary, _do not hesitate_ with that kill switch.”

“Alright, but that’s not going to happen—” Rodney began, but Elizabeth silenced him with a glare.

“John, could I speak to you alone for a moment?” Elizabeth asked.

“We’ll catch up with you,” John told the rest of the team.

Once the others had departed, Elizabeth said, “I want Zelenka to take Doctor McKay’s place on this mission. I don’t trust McKay to pull the trigger on the kill switch if it comes to that.”

John frowned. “I don’t trust McKay with the kill switch either, but if something goes wrong with the hyperdrive after the first jump, we may need him to make the repairs. I’d feel better if we had both of them along.”

Elizabeth shook her head. “If McKay’s there, Zelenka will defer to McKay on when to activate the kill switch instead of trusting his own judgment. Besides, Radek’s a lot smarter than we normally give him credit for. It’s high time we recognize that.”

“McKay does keep him pretty cowed, doesn’t he?” John admitted. “Alright. You want to tell him, or should I?”

“I’ll do it,” Elizabeth replied. “You’re the one who’ll still have to work with him after this mission is over. It’s probably better if you not ruin your working relationship with him any more than is absolutely necessary to get it through that thick skull of his that there are some things even he can’t do.”

John nodded. “Elizabeth…” _I love you,_ he wanted to say. _You know, I never really believed in ‘love at first sight,’ but then I met you, and…there’s really no other term I can come up with to describe it._ But he knew he would only be making it harder on both of them when the inevitable came. “I’m sorry it had to happen this way.”

Elizabeth wanted to place a hand on his shoulder to comfort him, but she didn’t dare risk the possibility of infecting him with nanites. “It’s alright, John. It’s not your fault Doctor McKay disobeyed you.”

She sighed before continuing, “I should’ve made a living will that said my nanites weren’t to be reactivated under any circumstances, even to save my life.”

John raised an eyebrow at her. “You really think knowing what you wanted would’ve stopped him?”

“I’d like to think it would’ve at least given him pause,” Elizabeth responded, “but even if it didn’t stop him, it might’ve stopped Doctor Keller from going along with his plan.”

There was a brief silence before John said, “Well, I’ll meet you in the Jumper bay?”

Elizabeth nodded. “See you then.”

* * *

John and Ronon bounded up the Jumper’s boarding ramp. When they reached the cockpit, Ronon handed Zelenka the case containing their stolen ZPM.

“Alright, get that hooked up and let’s get out of here,” John ordered.

“We can’t, not yet,” Elizabeth told him.

John looked at her in confusion. “Why not?”

“Now that I’ve linked with their database, it’s only a matter of time before the Replicators discover that my nanites are back online,” Elizabeth explained. “Once they do, they’ll be able to get a fix on my location. If I go back with you, I’d be leading them right to Atlantis.”

John nodded sadly. Turning to Zelenka, he asked, “If we activate the kill switch, the nanites will be completely shut down?”

Zelenka nodded. “The kill switch issues a command to each nanite that will result in its main processor overloading. They will be shut down with no possibility of ever being reactivated again.”

John exhaled in relief. “Then after we activate the kill switch, it’ll be safe to bring her body home with us.”

Zelenka nodded again. “Yes. Small consolation, I know, but it’s better than nothing.”

Elizabeth went over to Zelenka and looked him in the eye. “Radek, you are smarter than anyone in Atlantis gives you credit for. Don’t let Doctor McKay tell you otherwise.”

Zelenka wasn’t quite sure how to respond, eventually deciding on, “Thank you.”

Elizabeth next turned to the Satedan member of their team. “Ronon, it’s been a pleasure.”

“Yeah,” Ronon agreed. “Same here.”

That left only one more goodbye to say. “John…” _I love you,_ she wanted to tell him. _Even before Simon broke off our engagement, I’d have chosen you over him in a heartbeat if I’d had the opportunity._ But she knew it would only make this harder for both of them. “Keep our city safe.”

John struggled to keep his composure as he replied, “I will.”

Elizabeth then went into the back of the Jumper and lay down on one of the benches, closing her eyes and clasping her hands over her chest.

“Go ahead, Radek,” she ordered, schooling her features into a peaceful expression.

A single beep sounded from Zelenka’s tablet as he uploaded the command to her nanites. “_Sbohem_, Elizabeth. _Odpočívej v pokoji_.”

John, Ronon, and Zelenka watched in silence as the rise and fall of Elizabeth’s chest slowed and then, after a few minutes, stopped.

“How long until you can have the hyperdrive back online?” John asked Zelenka quietly.

Zelenka shrugged. “Fifteen, twenty minutes?”

John nodded. “Let me know when we’re ready to leave.”

Once Zelenka disappeared back into the front compartment, John knelt beside the bench on which Elizabeth’s body lay, took one lifeless hand in his, and wept.

**Author's Note:**

> Because Zelenka replaced McKay on the strike team, they didn’t discover and reactivate the Wraith attack command in the Replicator base code; however, this also has the result that instead of Elizabeth being captured by the Replicators and left to an uncertain fate, she dies peacefully and her body is able to be taken back to Earth and given a proper burial, so I think that’s a fair trade.
> 
> Obviously there are some issues left unaddressed by ending the story here, most notably McKay’s reactions to being left off the mission and to the decision to activate the kill switch before leaving the Replicator homeworld. I may write more in this AU in the future, but I wanted this story to be primarily about John and Elizabeth; McKay and their handling of his decision to reactivate the nanites actually wound up playing a much bigger part in this story than I originally envisioned.
> 
> Zelenka’s line in Czech at the end is supposed to be “Goodbye, Elizabeth. Rest in peace.” If that is not what it actually says, I would appreciate it if someone who speaks Czech could leave a comment with a corrected translation so that I can fix it.


End file.
